X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=6fce9847e02af1843fdfa933bb9e0f93a38610b3;hb=e67a74ee1dac618d941fce0fc5ef4561f76380b1;hp=47bec31ec7664889c8ad872dc410bd32cbbcf3e8;hpb=d2259df2688d404ac89f6dfed3921280a5038c7b;p=jalview.git

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 47bec31..6fce984 100644
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -28,10 +28,11 @@ import java.io.File;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.HashSet;
+import java.util.LinkedHashMap;
 import java.util.LinkedHashSet;
 import java.util.List;
 import java.util.Locale;
-import java.util.concurrent.Callable;
+import java.util.Map;
 import java.util.concurrent.Executors;
 
 import javax.swing.JCheckBox;
@@ -43,12 +44,20 @@ import javax.swing.JTable;
 import javax.swing.SwingUtilities;
 import javax.swing.table.AbstractTableModel;
 
+import com.stevesoft.pat.Regex;
+
+import jalview.analysis.AlignmentUtils;
+import jalview.api.AlignmentViewPanel;
 import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
 import jalview.bin.Console;
 import jalview.bin.Jalview;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
 import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.ext.jmol.JmolParser;
 import jalview.fts.api.FTSData;
 import jalview.fts.api.FTSDataColumnI;
 import jalview.fts.api.FTSRestClientI;
@@ -57,10 +66,12 @@ import jalview.fts.core.FTSRestRequest;
 import jalview.fts.core.FTSRestResponse;
 import jalview.fts.service.pdb.PDBFTSRestClient;
 import jalview.fts.service.threedbeacons.TDB_FTSData;
+import jalview.gui.StructureViewer.ViewerType;
 import jalview.gui.structurechooser.PDBStructureChooserQuerySource;
 import jalview.gui.structurechooser.StructureChooserQuerySource;
 import jalview.gui.structurechooser.ThreeDBStructureChooserQuerySource;
 import jalview.io.DataSourceType;
+import jalview.io.FileFormatException;
 import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
 import jalview.jbgui.FilterOption;
@@ -73,6 +84,8 @@ import jalview.util.Platform;
 import jalview.util.StringUtils;
 import jalview.ws.DBRefFetcher;
 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
+import jalview.ws.datamodel.alphafold.PAEContactMatrix;
+import jalview.ws.dbsources.EBIAlfaFold;
 import jalview.ws.seqfetcher.DbSourceProxy;
 import jalview.ws.sifts.SiftsSettings;
 
@@ -336,7 +349,7 @@ public class StructureChooser extends GStructureChooser
     };
 
     // fetch db refs if OK pressed
-    final Callable discoverCanonicalDBrefs = () -> {
+    final Runnable discoverCanonicalDBrefs = () -> {
       btn_queryTDB.setEnabled(false);
       populateSeqsWithoutSourceDBRef();
 
@@ -358,14 +371,12 @@ public class StructureChooser extends GStructureChooser
         // call finished action directly
         afterDbRefFetch.finished();
       }
-      return null;
     };
-    final Callable revertview = () -> {
+    final Runnable revertview = () -> {
       if (lastSelected != null)
       {
         cmb_filterOption.setSelectedItem(lastSelected);
       }
-      return null;
     };
     int threshold = Cache.getDefault("UNIPROT_AUTOFETCH_THRESHOLD",
             THRESHOLD_WARN_UNIPROT_FETCH_NEEDED);
@@ -679,13 +690,24 @@ public class StructureChooser extends GStructureChooser
     {
       selectedPdbFileName = chooser.getSelectedFile().getPath();
       Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
+      boolean guessTFType = localPdbPaeMatrixFileName == null;
       localPdbPaeMatrixFileName = guessPAEFilename();
+      guessTFType |= localPdbPaeMatrixFileName != null;
+      Regex alphaFold = JmolParser.getNewAlphafoldValidator();
+      if (guessTFType
+              && alphaFold.search(new File(selectedPdbFileName).getName())
+              && !tempFacAsChanged)
+      {
+        // localPdbPaeMatrixFileName was null and now isn't and filename could
+        // well be AlphaFold and user hasn't adjusted the tempFacType
+        combo_tempFacAs.setSelectedItem(TFType.PLDDT);
+      }
       validateSelections();
     }
   }
 
   /**
-   * Handles action event for btn_pdbFromFile
+   * Handles action event for btn_paeMatrixFile
    */
   @Override
   protected void paeMatrixFile_actionPerformed()
@@ -714,10 +736,26 @@ public class StructureChooser extends GStructureChooser
             "label.load_pae_matrix_file_associate_with_structure",
             pdbFile.getName()));
 
+    // TODO convert to Callable/Promise
     int value = chooser.showOpenDialog(null);
     if (value == JalviewFileChooser.APPROVE_OPTION)
     {
-      localPdbPaeMatrixFileName = chooser.getSelectedFile().getPath();
+      String fileName = chooser.getSelectedFile().getPath();
+      try
+      {
+        PAEContactMatrix.validateContactMatrixFile(fileName);
+      } catch (Exception thr)
+      {
+        JvOptionPane.showInternalMessageDialog(this, MessageManager
+                .formatMessage("label.couldnt_load_file", new Object[]
+                { fileName }) + "<br>" + thr.getLocalizedMessage(),
+                MessageManager.getString("label.error_loading_file"),
+                JvOptionPane.WARNING_MESSAGE);
+        Console.error("Couldn't import " + fileName + " as a PAE matrix",
+                thr);
+        return;
+      }
+      localPdbPaeMatrixFileName = fileName;
       Cache.setProperty("LAST_DIRECTORY", localPdbPaeMatrixFileName);
     }
     validateAssociationFromFile();
@@ -725,7 +763,9 @@ public class StructureChooser extends GStructureChooser
 
   private String guessPAEFilename()
   {
-    if (selectedPdbFileName.toLowerCase(Locale.ROOT).endsWith(".pdb"))
+    if (selectedPdbFileName.toLowerCase(Locale.ROOT).endsWith(".pdb")
+            || selectedPdbFileName.toLowerCase(Locale.ROOT)
+                    .endsWith(".cif"))
     {
       String jsonExt = selectedPdbFileName.substring(0,
               selectedPdbFileName.length() - 4) + ".json";
@@ -1037,11 +1077,13 @@ public class StructureChooser extends GStructureChooser
       {
         pdbFileString = MessageManager.getString("label.none");
         pdbFileTooltip = MessageManager.getString("label.nothing_selected");
+        setPdbOptionsEnabled(false);
       }
     }
     else
     {
       btn_pdbFromFile.setEnabled(false);
+      setPdbOptionsEnabled(false);
       // lbl_fromFileStatus.setIcon(errorImage);
       pdbFileString = MessageManager.getString("label.none");
       pdbFileTooltip = MessageManager.getString("label.nothing_selected");
@@ -1166,7 +1208,14 @@ public class StructureChooser extends GStructureChooser
     final StructureSelectionManager ssm = ap.getStructureSelectionManager();
 
     final int preferredHeight = pnl_filter.getHeight();
+    btn_add.setEnabled(false);
+    btn_newView.setEnabled(false);
+    btn_cancel.setEnabled(false);
+    actionsPanel.setEnabled(false);
 
+    final String progress = MessageManager
+            .getString("label.working_ellipsis");
+    setProgressBar(progress, progress.hashCode());
     Runnable viewStruc = new Runnable()
     {
       @Override
@@ -1250,26 +1299,28 @@ public class StructureChooser extends GStructureChooser
         }
         else if (currentView == VIEWS_FROM_FILE)
         {
-          SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel
-                  .getCmb_assSeq().getSelectedItem()).getSequence();
+          StructureChooser sc = StructureChooser.this;
+          TFType tft = (TFType) sc.combo_tempFacAs.getSelectedItem();
+          String paeFilename = sc.localPdbPaeMatrixFileName;
+          AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) fileChooserAssSeqPanel
+                  .getCmb_assSeq().getSelectedItem();
+          SequenceI userSelectedSeq = assSeqOpt.getSequence();
           if (userSelectedSeq != null)
           {
             selectedSequence = userSelectedSeq;
           }
-          PDBEntry fileEntry = new AssociatePdbFileWithSeq()
-                  .associatePdbWithSeq(selectedPdbFileName,
-                          DataSourceType.FILE, selectedSequence, true,
-                          Desktop.instance);
+          String pdbFilename = selectedPdbFileName;
 
-          sViewer = launchStructureViewer(ssm, new PDBEntry[] { fileEntry },
-                  ap, new SequenceI[]
-                  { selectedSequence });
+          StructureChooser.openStructureFileForSequence(ssm, sc, ap,
+                  selectedSequence, true, pdbFilename, tft, paeFilename,
+                  true);
         }
         SwingUtilities.invokeLater(new Runnable()
         {
           @Override
           public void run()
           {
+            setProgressBar("Complete.", progress.hashCode());
             closeAction(preferredHeight);
             mainFrame.dispose();
           }
@@ -1322,6 +1373,15 @@ public class StructureChooser extends GStructureChooser
           StructureSelectionManager ssm, final PDBEntry[] pdbEntriesToView,
           final AlignmentPanel alignPanel, SequenceI[] sequences)
   {
+    return launchStructureViewer(ssm, pdbEntriesToView, alignPanel,
+            sequences, null);
+  }
+
+  private StructureViewer launchStructureViewer(
+          StructureSelectionManager ssm, final PDBEntry[] pdbEntriesToView,
+          final AlignmentPanel alignPanel, SequenceI[] sequences,
+          ViewerType viewerType)
+  {
     long progressId = sequences.hashCode();
     setProgressBar(MessageManager
             .getString("status.launching_3d_structure_viewer"), progressId);
@@ -1386,14 +1446,17 @@ public class StructureChooser extends GStructureChooser
               MessageManager.getString(
                       "status.fetching_3d_structures_for_selected_entries"),
               progressId);
-      theViewer.viewStructures(pdbEntriesToView, sequences, alignPanel);
+      theViewer.viewStructures(pdbEntriesToView, sequences, alignPanel,
+              viewerType);
     }
     else
     {
       setProgressBar(MessageManager.formatMessage(
               "status.fetching_3d_structures_for",
               pdbEntriesToView[0].getId()), progressId);
-      theViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
+      // Can we pass a pre-computeMappinged pdbFile?
+      theViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel,
+              viewerType);
     }
     setProgressBar(null, progressId);
     // remember the last viewer we used...
@@ -1634,20 +1697,21 @@ public class StructureChooser extends GStructureChooser
   @Override
   public void setProgressBar(String message, long id)
   {
-    if (!Platform.isHeadless())
+    if (!Platform.isHeadless() && progressBar != null)
       progressBar.setProgressBar(message, id);
   }
 
   @Override
   public void registerHandler(long id, IProgressIndicatorHandler handler)
   {
-    progressBar.registerHandler(id, handler);
+    if (progressBar != null)
+      progressBar.registerHandler(id, handler);
   }
 
   @Override
   public boolean operationInProgress()
   {
-    return progressBar.operationInProgress();
+    return progressBar == null ? false : progressBar.operationInProgress();
   }
 
   public JalviewStructureDisplayI getOpenedStructureViewer()
@@ -1691,30 +1755,76 @@ public class StructureChooser extends GStructureChooser
   /**
    * Open a single structure file for a given sequence
    */
-  public static void openStructureFileForSequence(AlignmentPanel ap,
-          SequenceI seq, File sFile)
+  public static void openStructureFileForSequence(
+          StructureSelectionManager ssm, StructureChooser sc,
+          AlignmentPanel ap, SequenceI seq, boolean prompt,
+          String sFilename, TFType tft, String paeFilename,
+          boolean doXferSettings)
   {
-    // Open the chooser headlessly. Not sure this is actually needed ?
-    StructureChooser sc = new StructureChooser(new SequenceI[] { seq }, seq,
-            ap, false);
-    StructureSelectionManager ssm = ap.getStructureSelectionManager();
-    PDBEntry fileEntry = null;
-    try
-    {
-      fileEntry = new AssociatePdbFileWithSeq().associatePdbWithSeq(
-              sFile.getAbsolutePath(), DataSourceType.FILE, seq, true,
-              Desktop.instance);
-    } catch (Exception e)
-    {
-      Console.error("Could not open structure file '"
-              + sFile.getAbsolutePath() + "'");
-      return;
+    openStructureFileForSequence(ssm, sc, ap, seq, prompt, sFilename, tft,
+            paeFilename, false, true, doXferSettings, null);
+  }
+
+  public static StructureViewer openStructureFileForSequence(
+          StructureSelectionManager ssm, StructureChooser sc,
+          AlignmentPanel ap, SequenceI seq, boolean prompt,
+          String sFilename, TFType tft, String paeFilename,
+          boolean forceHeadless, boolean showRefAnnotations,
+          boolean doXferSettings, ViewerType viewerType)
+  {
+    StructureViewer sv = null;
+    boolean headless = forceHeadless;
+    if (sc == null)
+    {
+      // headless = true;
+      prompt = false;
+      sc = new StructureChooser(new SequenceI[] { seq }, seq, ap, false);
+    }
+    if (ssm == null)
+    {
+      ssm = ap.getStructureSelectionManager();
     }
 
-    StructureViewer sViewer = sc.launchStructureViewer(ssm,
-            new PDBEntry[]
-            { fileEntry }, ap, new SequenceI[] { seq });
+    PDBEntry fileEntry = new AssociatePdbFileWithSeq().associatePdbWithSeq(
+            sFilename, DataSourceType.FILE, seq, prompt, Desktop.instance,
+            tft, paeFilename, doXferSettings);
+
+    // if headless, "false" in the sc constructor above will avoid GUI behaviour
+    // in sc.launchStructureViewer()
+    if (!headless && !(viewerType == null))
+    {
+      sv = sc.launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap,
+              new SequenceI[]
+              { seq }, viewerType);
+    }
 
     sc.mainFrame.dispose();
+
+    if (showRefAnnotations)
+      showReferenceAnnotationsForSequence(ap.alignFrame, seq);
+
+    return sv;
+  }
+
+  public static void showReferenceAnnotationsForSequence(AlignFrame af,
+          SequenceI sequence)
+  {
+    AlignViewport av = af.getCurrentView();
+    AlignmentI al = av.getAlignment();
+
+    List<SequenceI> forSequences = new ArrayList<>();
+    forSequences.add(sequence);
+    final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<>();
+    AlignmentUtils.findAddableReferenceAnnotations(forSequences, null,
+            candidates, al);
+    final SequenceGroup selectionGroup = av.getSelectionGroup();
+    AlignmentUtils.addReferenceAnnotations(candidates, al, selectionGroup);
+    for (AlignmentViewPanel ap : af.getAlignPanels())
+    {
+      // required to readjust the height and position of the PAE
+      // annotation
+      ap.adjustAnnotationHeight();
+    }
+
   }
 }